add record for iPTMnet API #89
Description
Data Source
Optional. Name of the preferred source for this data. E.g. OMIM, DrugBank
- iPTMnet -- more info at https://research.bioinformatics.udel.edu/iptmnet/
Main Entity Type
What kind of entity are you interested in? Biolink type preferred, e.g. variant, disease, gene
- SUBJECT: Protein
Connected Entity Type
What kind of thing should the subject be connected to? E.g. for drug-disease links this would be 'disease'. Biolink type preferred
-
OBJECT: Protein
-
RELATION: entity regulated by entity / entity regulates entity
Example statement
Enter one or more examples of statements/edges you would expect to retrieve using this source. For example, "aldehydes exacerbates Fanconi anemia". In future this could be used to drive integration tests
- EXAMPLE 1: CDK2 is phosphorylated by CDK7
From https://research.bioinformatics.udel.edu/iptmnet/api/P24941/substrate, this snippet asserts that CDK7 phosphorylates CDK2 with various bits of provenance
{
"residue": "T",
"site": "T165",
"ptm_type": "Phosphorylation",
"score": 3,
"sources": [
{
"name": "RLIMS-P",
"label": "rlimsp",
"url": "http://research.bioinformatics.udel.edu/rlimsp/"
},
{
"name": "PSP",
"label": "psp",
"url": "http://www.phosphosite.org/"
}
],
"enzymes": [
{
"id": "P50613",
"enz_type": "uniprot_ac",
"name": "CDK7"
}
],
"pmids": [
"18396144"
]
}
- EXAMPLE 2: CDK2 phosphorylates MCM4
From https://research.bioinformatics.udel.edu/iptmnet/api/P24941/as-enzyme, this snippet asserts that CDK2 phosphorylates MCM4 with various bits of provenance
{
"substrate": "P33991",
"substrate_symbol": "MCM4",
"site": "S3",
"score": 0,
"sources": [
{
"name": "HPRD",
"label": "hprd",
"url": "http://www.hprd.org/"
}
],
"pmids": [
"19651622",
"16519687",
"20068231"
]
}
Preferred format or ingest method
How would you prefer to get the data? Via API or Data dump that can be ingested into your KG? Would you prefer a smart API registry entry, a neo4j dump, biolink-compliant CSV/RDF/JSON that can be loaded with KGX?
- METHOD: SmartAPI annotation -- note existing Swagger documentation at https://research.bioinformatics.udel.edu/iptmnet/api/doc/